Mercurial > repos > azomics > check_fcs_header

annotate getFCSheader.R @ 0:2227def10ea4 draft default tip

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"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/check_fcs_headers commit 6da41781e60ad4e264c4d725c5373b099b4766d4"
author azomics
date Wed, 24 Jun 2020 17:36:27 -0400
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2227def10ea4 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/check_fcs_headers commit 6da41781e60ad4e264c4d725c5373b099b4766d4"
azomics
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1 #!/usr/bin/Rscript --vanilla
2227def10ea4 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/check_fcs_headers commit 6da41781e60ad4e264c4d725c5373b099b4766d4"
azomics
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2 # FCS Headers Module for Galaxy
2227def10ea4 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/check_fcs_headers commit 6da41781e60ad4e264c4d725c5373b099b4766d4"
azomics
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3 # FlowCore
2227def10ea4 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/check_fcs_headers commit 6da41781e60ad4e264c4d725c5373b099b4766d4"
azomics
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4 ######################################################################
2227def10ea4 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/check_fcs_headers commit 6da41781e60ad4e264c4d725c5373b099b4766d4"
azomics
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5 # Copyright (c) 2016 Northrop Grumman.
2227def10ea4 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/check_fcs_headers commit 6da41781e60ad4e264c4d725c5373b099b4766d4"
azomics
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6 # All rights reserved.
2227def10ea4 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/check_fcs_headers commit 6da41781e60ad4e264c4d725c5373b099b4766d4"
azomics
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7 ######################################################################
2227def10ea4 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/check_fcs_headers commit 6da41781e60ad4e264c4d725c5373b099b4766d4"
azomics
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8 #
2227def10ea4 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/check_fcs_headers commit 6da41781e60ad4e264c4d725c5373b099b4766d4"
azomics
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9 # Version 2
2227def10ea4 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/check_fcs_headers commit 6da41781e60ad4e264c4d725c5373b099b4766d4"
azomics
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10 # May 2018
2227def10ea4 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/check_fcs_headers commit 6da41781e60ad4e264c4d725c5373b099b4766d4"
azomics
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11 # Cristel Thomas
2227def10ea4 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/check_fcs_headers commit 6da41781e60ad4e264c4d725c5373b099b4766d4"
azomics
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12 #
2227def10ea4 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/check_fcs_headers commit 6da41781e60ad4e264c4d725c5373b099b4766d4"
azomics
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13 #
2227def10ea4 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/check_fcs_headers commit 6da41781e60ad4e264c4d725c5373b099b4766d4"
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14
2227def10ea4 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/check_fcs_headers commit 6da41781e60ad4e264c4d725c5373b099b4766d4"
azomics
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15 library(flowCore)
2227def10ea4 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/check_fcs_headers commit 6da41781e60ad4e264c4d725c5373b099b4766d4"
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16
2227def10ea4 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/check_fcs_headers commit 6da41781e60ad4e264c4d725c5373b099b4766d4"
azomics
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17 getFCSChannels <- function(input_fcs) {
2227def10ea4 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/check_fcs_headers commit 6da41781e60ad4e264c4d725c5373b099b4766d4"
azomics
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18 fcs <- read.FCS(input_fcs, transformation=F)
2227def10ea4 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/check_fcs_headers commit 6da41781e60ad4e264c4d725c5373b099b4766d4"
azomics
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19 return(colnames(fcs))
2227def10ea4 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/check_fcs_headers commit 6da41781e60ad4e264c4d725c5373b099b4766d4"
azomics
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20 }
2227def10ea4 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/check_fcs_headers commit 6da41781e60ad4e264c4d725c5373b099b4766d4"
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21
2227def10ea4 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/check_fcs_headers commit 6da41781e60ad4e264c4d725c5373b099b4766d4"
azomics
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22 getFCSMarkers <- function(input_fcs){
2227def10ea4 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/check_fcs_headers commit 6da41781e60ad4e264c4d725c5373b099b4766d4"
azomics
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23 ffcs <- read.FCS(input_fcs, transformation=F)
2227def10ea4 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/check_fcs_headers commit 6da41781e60ad4e264c4d725c5373b099b4766d4"
azomics
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24 fmarkers <- as.vector(pData(parameters(ffcs))$desc)
2227def10ea4 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/check_fcs_headers commit 6da41781e60ad4e264c4d725c5373b099b4766d4"
azomics
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25 return(fmarkers)
2227def10ea4 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/check_fcs_headers commit 6da41781e60ad4e264c4d725c5373b099b4766d4"
azomics
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26 }
2227def10ea4 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/check_fcs_headers commit 6da41781e60ad4e264c4d725c5373b099b4766d4"
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27
2227def10ea4 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/check_fcs_headers commit 6da41781e60ad4e264c4d725c5373b099b4766d4"
azomics
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28 getFCSMarkerNames <- function(output_file="", file_paths=vector(),
2227def10ea4 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/check_fcs_headers commit 6da41781e60ad4e264c4d725c5373b099b4766d4"
azomics
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29 fcs_names=vector()) {
2227def10ea4 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/check_fcs_headers commit 6da41781e60ad4e264c4d725c5373b099b4766d4"
azomics
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30 check_files <- sapply(file_paths, isFCSfile)
2227def10ea4 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/check_fcs_headers commit 6da41781e60ad4e264c4d725c5373b099b4766d4"
azomics
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31 channels <- lapply(file_paths[check_files], getFCSChannels)
2227def10ea4 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/check_fcs_headers commit 6da41781e60ad4e264c4d725c5373b099b4766d4"
azomics
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32 markers <- lapply(file_paths[check_files], getFCSMarkers)
2227def10ea4 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/check_fcs_headers commit 6da41781e60ad4e264c4d725c5373b099b4766d4"
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33
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azomics
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34 nb_col <- max(lengths(channels))
2227def10ea4 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/check_fcs_headers commit 6da41781e60ad4e264c4d725c5373b099b4766d4"
azomics
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35 nc <- lapply(channels, `length<-`, nb_col)
2227def10ea4 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/check_fcs_headers commit 6da41781e60ad4e264c4d725c5373b099b4766d4"
azomics
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36 ct <- t(as.data.frame(nc))
2227def10ea4 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/check_fcs_headers commit 6da41781e60ad4e264c4d725c5373b099b4766d4"
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37
2227def10ea4 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/check_fcs_headers commit 6da41781e60ad4e264c4d725c5373b099b4766d4"
azomics
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38 nm <- lapply(markers, `length<-`, nb_col)
2227def10ea4 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/check_fcs_headers commit 6da41781e60ad4e264c4d725c5373b099b4766d4"
azomics
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39 mt <- t(as.data.frame(nm))
2227def10ea4 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/check_fcs_headers commit 6da41781e60ad4e264c4d725c5373b099b4766d4"
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2227def10ea4 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/check_fcs_headers commit 6da41781e60ad4e264c4d725c5373b099b4766d4"
azomics
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41 nb_files <- sum(check_files)
2227def10ea4 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/check_fcs_headers commit 6da41781e60ad4e264c4d725c5373b099b4766d4"
azomics
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42 Index <- rep(c("channels", "markers"), each=nb_files)
2227def10ea4 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/check_fcs_headers commit 6da41781e60ad4e264c4d725c5373b099b4766d4"
azomics
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43 Filename <- rep(fcs_names[check_files], 2)
2227def10ea4 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/check_fcs_headers commit 6da41781e60ad4e264c4d725c5373b099b4766d4"
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44
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azomics
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45 idx_nb <- seq(nb_col)
2227def10ea4 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/check_fcs_headers commit 6da41781e60ad4e264c4d725c5373b099b4766d4"
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46 ttt <- rbind(ct,mt)
2227def10ea4 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/check_fcs_headers commit 6da41781e60ad4e264c4d725c5373b099b4766d4"
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47 finalt <- cbind(Filename, Index, ttt)
2227def10ea4 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/check_fcs_headers commit 6da41781e60ad4e264c4d725c5373b099b4766d4"
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48 colnames(finalt)[3:length(colnames(finalt))] <- idx_nb
2227def10ea4 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/check_fcs_headers commit 6da41781e60ad4e264c4d725c5373b099b4766d4"
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49
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50
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51 if (nb_files != length(file_paths)){
2227def10ea4 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/check_fcs_headers commit 6da41781e60ad4e264c4d725c5373b099b4766d4"
azomics
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52 not_fcs <- fcs_names[!check_files]
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azomics
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53 new_df <- cbind(not_fcs, "Not a valid FCS file")
2227def10ea4 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/check_fcs_headers commit 6da41781e60ad4e264c4d725c5373b099b4766d4"
azomics
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54 empty_frame <- data.frame(matrix("", nrow=length(not_fcs), ncol=nb_col),
2227def10ea4 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/check_fcs_headers commit 6da41781e60ad4e264c4d725c5373b099b4766d4"
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55 stringsAsFactors = F)
2227def10ea4 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/check_fcs_headers commit 6da41781e60ad4e264c4d725c5373b099b4766d4"
azomics
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56 not_fcs_files <- cbind(new_df, empty_frame)
2227def10ea4 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/check_fcs_headers commit 6da41781e60ad4e264c4d725c5373b099b4766d4"
azomics
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57 colnames(not_fcs_files) <- colnames(finalt)
2227def10ea4 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/check_fcs_headers commit 6da41781e60ad4e264c4d725c5373b099b4766d4"
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58 new_final <- rbind(finalt, not_fcs_files)
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59 write.table(new_final, file=output_file, quote=F, row.names=F, col.names=T,
2227def10ea4 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/check_fcs_headers commit 6da41781e60ad4e264c4d725c5373b099b4766d4"
azomics
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60 sep='\t', append=F)
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61 quit(save = "no", status = 10, runLast = FALSE)
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azomics
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62 } else {
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63 # output file
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64 write.table(finalt, file=output_file, quote=F, row.names=F, col.names=T,
2227def10ea4 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/check_fcs_headers commit 6da41781e60ad4e264c4d725c5373b099b4766d4"
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65 sep='\t',
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66 append=F)
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67 }
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68 }
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69
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70 ################################################################################
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azomics
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71 ################################################################################
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72
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73 args <- commandArgs(trailingOnly = TRUE)
2227def10ea4 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/check_fcs_headers commit 6da41781e60ad4e264c4d725c5373b099b4766d4"
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74
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75 i <- 1
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azomics
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76 nb_files <- (length(args)-1) / 2
2227def10ea4 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/check_fcs_headers commit 6da41781e60ad4e264c4d725c5373b099b4766d4"
azomics
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77 fcs_files <- character(nb_files)
2227def10ea4 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/check_fcs_headers commit 6da41781e60ad4e264c4d725c5373b099b4766d4"
azomics
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78 fcs_names <- character(nb_files)
2227def10ea4 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/check_fcs_headers commit 6da41781e60ad4e264c4d725c5373b099b4766d4"
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79 for (j in 1:length(args)){
2227def10ea4 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/check_fcs_headers commit 6da41781e60ad4e264c4d725c5373b099b4766d4"
azomics
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80 if (!j%%2){
2227def10ea4 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/check_fcs_headers commit 6da41781e60ad4e264c4d725c5373b099b4766d4"
azomics
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81 fcs_files[[i]] <- args[[j]]
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azomics
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82 fcs_names[[i]]<- args[[j+1]]
2227def10ea4 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/check_fcs_headers commit 6da41781e60ad4e264c4d725c5373b099b4766d4"
azomics
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83 i <- i + 1
2227def10ea4 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/check_fcs_headers commit 6da41781e60ad4e264c4d725c5373b099b4766d4"
azomics
parents:
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84 }
2227def10ea4 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/check_fcs_headers commit 6da41781e60ad4e264c4d725c5373b099b4766d4"
azomics
parents:
diff changeset
85 }
2227def10ea4 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/check_fcs_headers commit 6da41781e60ad4e264c4d725c5373b099b4766d4"
azomics
parents:
diff changeset
86
2227def10ea4 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/check_fcs_headers commit 6da41781e60ad4e264c4d725c5373b099b4766d4"
azomics
parents:
diff changeset
87 getFCSMarkerNames(args[1], fcs_files, fcs_names)